# HG changeset patch
# User malbuquerque
# Date 1421781403 18000
# Node ID ace1798624b47cac373c226a0aaaba4b140bd665
Uploaded
diff -r 000000000000 -r ace1798624b4 package/delly.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/package/delly.xml Tue Jan 20 14:16:43 2015 -0500
@@ -0,0 +1,106 @@
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+ structural variant discovery by integrated paired-end and split-read analysis
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+ delly
+ DELLY_DIR
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+ #for $i, $s in enumerate( $repeatBam )
+ ln -s $s.sortedBam ./input$(i).bam;
+ ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai;
+ #end for
+
+
+ #if not isinstance( $type.value, list ):
+ #set $args = [ $type.value ]
+ #else:
+ #set $args = $type.value
+ #end if
+
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+ #for $option in $args
+
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+ \$DELLY_DIR/src/delly -t $option -o ./output.$(option).vcf -q $mapQual -s $madCutoff
+ #if $option == "DEL"
+ -m $minFlank
+ #end if
+ -u $genoQual -v $vcfgeno -g $genome
+
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+ #for $i, $s in enumerate( $repeatBam )
+ ./input$(i).bam
+ #end for
+ ;
+ #end for
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+ #set $option = $args[0]
+ grep ^\# output.$(option).vcf > $outfile;
+ grep ^\# -v output.$(option).vcf > variants.txt;
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+ #if isinstance( $type.value, list ):
+ #for $option in $args[1:]
+ grep ^\# -v output.$(option).vcf >> variants.txt;
+ #end for
+ #end if
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+ sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt;
+
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+ #if $filterCalls
+ awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile;
+ #else
+ cat sortedVariants.txt >> $outfile;
+ #end if
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diff -r 000000000000 -r ace1798624b4 package/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/package/tool_dependencies.xml Tue Jan 20 14:16:43 2015 -0500
@@ -0,0 +1,33 @@
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+ https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz
+ https://github.com/morinlab/galaxy_tools/delly/Makefile
+ make all BOOST_ROOT=\$BOOST_ROOT BAMTOOLS_ROOT=\$BAMTOOLS_ROOT SEQTK_ROOT=\$SEQTK_ROOT
+
+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR
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